Zinc in PDB 8w6p: Crystal Structure of Dimeric Murine SMPDL3A

The structure of Crystal Structure of Dimeric Murine SMPDL3A, PDB code: 8w6p was solved by C.Zhang, P.Liu, S.Fan, Y.Hou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.27 / 1.91
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	122.225, 122.225, 79.557, 90, 90, 90
R / Rfree (%)	21.8 / 24.6

The binding sites of Zinc atom in the Crystal Structure of Dimeric Murine SMPDL3A (pdb code 8w6p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Dimeric Murine SMPDL3A, PDB code: 8w6p:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Dimeric Murine SMPDL3A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Dimeric Murine SMPDL3A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:33.8 occ:1.00 O A:HOH643 1.9 24.5 1.0 OP1 A:YA4501 2.1 26.0 0.6 OD1 A:ASN148 2.2 20.8 1.0 NE2 A:HIS249 2.3 15.8 1.0 ND1 A:HIS290 2.3 22.9 1.0 OD2 A:ASP107 2.4 20.0 1.0 CE1 A:HIS290 3.1 27.0 1.0 CE1 A:HIS249 3.2 20.3 1.0 CG A:ASN148 3.2 20.0 1.0 CD2 A:HIS249 3.3 18.7 1.0 P A:YA4501 3.3 34.5 1.0 CG A:ASP107 3.4 22.0 1.0 ZN A:ZN505 3.4 25.6 1.0 CG A:HIS290 3.4 17.3 1.0 ND2 A:ASN148 3.7 24.5 1.0 OP3 A:YA4501 3.7 25.2 1.0 OD1 A:ASP107 3.8 18.4 1.0 CB A:HIS290 3.9 20.6 1.0 CA A:HIS290 3.9 20.2 1.0 OD1 A:ASP42 4.1 23.0 1.0 O A:HIS290 4.1 20.0 1.0 O5' A:YA4501 4.1 37.0 0.9 C5' A:YA4501 4.2 34.1 0.8 NE2 A:HIS290 4.3 22.7 1.0 ND1 A:HIS249 4.3 21.1 1.0 CD2 A:HIS149 4.4 21.8 1.0 CG A:HIS249 4.4 18.8 1.0 CD2 A:HIS290 4.5 18.1 1.0 N A:ASN148 4.5 18.5 1.0 C A:HIS290 4.5 19.2 1.0 CB A:ASN148 4.5 19.1 1.0 CB A:ASP107 4.6 20.7 1.0 SP3 A:YA4501 4.9 30.9 0.5

Zinc binding site 2 out of 4 in the Crystal Structure of Dimeric Murine SMPDL3A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Dimeric Murine SMPDL3A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:25.6 occ:1.00 OD1 A:ASP42 2.1 23.0 1.0 NE2 A:HIS44 2.2 19.4 1.0 NE2 A:HIS292 2.3 19.6 1.0 O A:HOH643 2.4 24.5 1.0 OD2 A:ASP107 2.4 20.0 1.0 OP3 A:YA4501 2.5 25.2 1.0 CD2 A:HIS44 3.2 18.9 1.0 CE1 A:HIS44 3.2 20.5 1.0 CE1 A:HIS292 3.2 23.9 1.0 CG A:ASP42 3.2 22.8 1.0 CD2 A:HIS292 3.3 20.6 1.0 CG A:ASP107 3.4 22.0 1.0 ZN A:ZN504 3.4 33.8 1.0 CB A:ASP107 3.6 20.7 1.0 P A:YA4501 3.7 34.5 1.0 OP1 A:YA4501 3.8 26.0 0.6 CB A:ASP42 3.8 20.0 1.0 CE1 A:HIS249 4.2 20.3 1.0 OD2 A:ASP42 4.2 21.6 1.0 O A:HIS290 4.3 20.0 1.0 ND1 A:HIS44 4.3 22.1 1.0 NE2 A:HIS249 4.3 15.8 1.0 CG A:HIS44 4.3 21.0 1.0 ND1 A:HIS292 4.3 22.4 1.0 NE2 A:HIS111 4.4 26.4 1.0 C5' A:YA4501 4.4 34.1 0.8 CG A:HIS292 4.4 20.8 1.0 CE1 A:HIS111 4.5 25.4 1.0 O5' A:YA4501 4.5 37.0 0.9 OD1 A:ASP107 4.5 18.4 1.0 CA A:ASP42 4.5 21.6 1.0 CA A:HIS290 4.6 20.2 1.0 CD2 A:HIS149 4.7 21.8 1.0 C A:HIS290 4.9 19.2 1.0 O4' A:YA4501 5.0 35.5 0.3

Zinc binding site 3 out of 4 in the Crystal Structure of Dimeric Murine SMPDL3A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Dimeric Murine SMPDL3A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn507 b:29.6 occ:1.00 OD1 B:ASP42 2.1 18.9 1.0 NE2 B:HIS292 2.3 22.4 1.0 NE2 B:HIS44 2.3 23.0 1.0 OD2 B:ASP107 2.3 18.2 1.0 O2 B:PO4506 2.4 28.2 1.0 O B:HOH639 2.5 23.3 1.0 O B:HOH604 2.6 37.2 1.0 CG B:ASP42 3.1 23.0 1.0 CD2 B:HIS44 3.2 23.4 1.0 CE1 B:HIS292 3.3 22.0 1.0 CD2 B:HIS292 3.3 18.5 1.0 CG B:ASP107 3.4 22.8 1.0 CE1 B:HIS44 3.4 24.8 1.0 ZN B:ZN508 3.4 36.9 1.0 CB B:ASP107 3.6 23.0 1.0 P B:PO4506 3.7 36.8 1.0 CB B:ASP42 3.7 22.0 1.0 O1 B:PO4506 3.9 28.5 1.0 OD2 B:ASP42 4.1 19.9 1.0 O4 B:PO4506 4.2 35.0 1.0 CE1 B:HIS249 4.2 20.2 1.0 NE2 B:HIS111 4.2 29.6 1.0 O B:HIS290 4.3 20.6 1.0 CG B:HIS44 4.4 23.5 1.0 ND1 B:HIS292 4.4 19.7 1.0 CG B:HIS292 4.4 20.9 1.0 ND1 B:HIS44 4.4 24.4 1.0 CE1 B:HIS111 4.4 28.3 1.0 NE2 B:HIS249 4.4 18.9 1.0 OD1 B:ASP107 4.5 21.9 1.0 CA B:ASP42 4.6 23.0 1.0 CA B:HIS290 4.7 22.2 1.0 CD2 B:HIS149 4.8 23.0 1.0 O3 B:PO4506 4.9 34.1 1.0 C B:HIS290 4.9 19.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Dimeric Murine SMPDL3A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Dimeric Murine SMPDL3A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn508 b:36.9 occ:1.00 O B:HOH639 1.9 23.3 1.0 O1 B:PO4506 2.2 28.5 1.0 NE2 B:HIS249 2.3 18.9 1.0 ND1 B:HIS290 2.3 19.9 1.0 OD1 B:ASN148 2.4 23.2 1.0 OD2 B:ASP107 2.5 18.2 1.0 CE1 B:HIS290 3.0 22.7 1.0 CE1 B:HIS249 3.1 20.2 1.0 P B:PO4506 3.3 36.8 1.0 CD2 B:HIS249 3.3 20.8 1.0 CG B:ASN148 3.3 23.5 1.0 CG B:HIS290 3.4 22.5 1.0 ZN B:ZN507 3.4 29.6 1.0 CG B:ASP107 3.4 22.8 1.0 O2 B:PO4506 3.5 28.2 1.0 ND2 B:ASN148 3.7 23.7 1.0 O B:HOH604 3.7 37.2 1.0 OD1 B:ASP107 3.8 21.9 1.0 CA B:HIS290 3.8 22.2 1.0 CB B:HIS290 3.8 19.5 1.0 O4 B:PO4506 3.8 35.0 1.0 OD1 B:ASP42 3.9 18.9 1.0 O B:HIS290 4.0 20.6 1.0 NE2 B:HIS290 4.2 20.3 1.0 ND1 B:HIS249 4.3 20.4 1.0 CD2 B:HIS149 4.3 23.0 1.0 C B:HIS290 4.4 19.0 1.0 CG B:HIS249 4.4 21.1 1.0 CD2 B:HIS290 4.4 23.4 1.0 O3 B:PO4506 4.5 34.1 1.0 N B:ASN148 4.7 20.6 1.0 CB B:ASP107 4.7 23.0 1.0 CB B:ASN148 4.7 21.1 1.0 N B:HIS290 4.9 17.3 1.0 NE2 B:HIS149 4.9 28.1 1.0

Y.Hou, Z.Wang, P.Liu, X.Wei, Z.Zhang, S.Fan, L.Zhang, F.Han, Y.Song, L.Chu, C.Zhang. SMPDL3A Is A Cgamp-Degrading Enzyme Induced By Lxr-Mediated Lipid Metabolism to Restrict Cgas-Sting Dna Sensing. Immunity V. 56 2492 2023.
ISSN: ISSN 1074-7613
PubMed: 37890481
DOI: 10.1016/J.IMMUNI.2023.10.001